BNC2 p.Val167=
c.501C>T · rs143821778 · VCV120241
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0293%, afr)
Conditions
1
hypotensive disorder
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -0.28 | GERP -4.2, phastCons 0.15 |
| Overall | ||
| CADD | 9.777 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0293%
African / African-American · 22/75,056 alleles
Filtering AF
0.0198%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0167%
Overall
0.00229%
37/1,614,196 alleles · ultra-rare
exomes 31/1,461,882 · genomes 6/152,314 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.0293% | 3,412 |
| Remaining individualsnot grpmax-eligible | 0.0112% | 8,930 |
| Admixed American | 0.00167% | 60,026 |
| European (non-Finnish) | 0.000593% | 168,577 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BNC2
- Protein
- p.Val167=
- Coding
- c.501C>T
- MANE Select
- NM_017637
- dbSNP
- rs143821778
- Type
- single nucleotide variant
- Location
- chr9:16552698 (GRCh38)
- Gene constraint
- LOEUF 0.365 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 54.10
Similar variants
- BNC2 p.Ala28= Benign ★★ same condition
- BNC2 p.Ala923Val Benign/Likely benign ★★ same condition
- BNC2 p.Asp930Gly Likely benign ★★ same condition
- BNC2 p.Ile974Val Benign ★★ same condition
- BNC2 p.Leu414Val Benign ★★ same condition
- BNC2 p.Leu826= Benign/Likely benign ★★ same condition
- BNC2 p.Phe312= Benign ★★ same condition
- BNC2 p.Pro623His Benign/Likely benign ★★ same condition
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bnc2-p-val167 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown